well, browsing through the source i found a
fullEncode variable that forces encoding, no matter for options.
this variable was used on page generator.
i just don't remember why i introduced it. 
i will try to disable it and see what happens. (in next 1.6 test release)
can you set on default the tray icon does not check "Tray Icon for each download" ? it fills up your system tray when people using flashget to download in muilt-part download
i understand that you need to disable that option, but this is not a good reason to have it disabled by default to anyone else.